Cloned drive, windows 7 64 bit

New computer, I have a E-sata dock, runs from a e-sata pci-e card recently installed. I put fresh formatted hard drive in dock, computer see's it fine, device manager also. Everything is fine.
I cloned the drive using casper, clone from primary C: drive to external drive. Once its cloned, computer won't show drive, but device manager does, It cloned fine, I swapped drives in PC, boots fine, everything great..Weird..If I put same drive on USB connection, same thing. But if I put cloned drive direct to extra sata port off mother board, computer shows it fine. Seems hooking up a clone of your boot drive to E-sata or usb won't show the drive on computer, but device manager shows it.